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AlignmentEndTrimmer

Bug fix: mismatches are now counted properly on the reverse strand
VCFParser
Added support for awful varcsan VCF output.

tmosbruger 2014-08-07

changed /trunk/Source/edu/utah/seq/parsers/AlignmentEndTrimmer.java
changed /trunk/Source/edu/utah/seq/vcf/VCFAnnotator.java
changed /trunk/Source/edu/utah/seq/vcf/VCFParser.java
changed /trunk/Source/edu/utah/seq/vcf/VCFRecord.java
changed /trunk/Source/edu/utah/seq/vcf/VCFReporter.java
changed /trunk/Source/edu/utah/seq/vcf/VCFSample.java
/trunk/Source/edu/utah/seq/parsers/AlignmentEndTrimmer.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFAnnotator.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFParser.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFRecord.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFReporter.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFSample.java Diff Switch to side-by-side view
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